I can only get my 9'er to start when it's in neutral. As I remember, if the bike is in gear and the kick stand is up, I should be able to start it if the clutch handle is fully depressed.
I have noticed that when idling (in neutral) the bike sits at a lower RPM than when in gear with the clutch lever all the way in. Also, when going from neutral to first, there's a pretty hefty 'clunk' sound.
I'm thinking my clutch cable needs to be adjusted? Is it possible that it's not providing enough pull from the handle?
The switch is on the back side of the side stand pivot, held on by a bolt. look or feel for it, you will see/feel a wire harness, follow the wires to the connector, check continuity with the stand down, you should NOT have continuity with the stand down, there will be continuity with the stand up. from the FSM, it looks like you can remove the bolt to inspect/change the switch, try cleaning it.